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- PDB-4gwr: Crystal Structure of the second catalytic domain of protein disul... -

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Basic information

Entry
Database: PDB / ID: 4gwr
TitleCrystal Structure of the second catalytic domain of protein disulfide isomerase P5
ComponentsProtein disulfide-isomerase A6
KeywordsISOMERASE / thioredoxin-like fold / disulfide isomerase / BiP / endoplasmic reticulum
Function / homology
Function and homology information


protein disulfide-isomerase / endoplasmic reticulum chaperone complex / XBP1(S) activates chaperone genes / protein disulfide isomerase activity / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome ...protein disulfide-isomerase / endoplasmic reticulum chaperone complex / XBP1(S) activates chaperone genes / protein disulfide isomerase activity / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / protein folding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular space / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein disulfide-isomerase A6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsVinaik, R. / Kozlov, G. / Gehring, K.
CitationJournal: To be Published / Year: 2013
Title: To be published
Authors: Vinaik, R. / Kozlov, G. / Gehring, K.
History
DepositionSep 3, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase A6
B: Protein disulfide-isomerase A6


Theoretical massNumber of molelcules
Total (without water)27,7792
Polymers27,7792
Non-polymers00
Water1,60389
1
A: Protein disulfide-isomerase A6


Theoretical massNumber of molelcules
Total (without water)13,8901
Polymers13,8901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein disulfide-isomerase A6


Theoretical massNumber of molelcules
Total (without water)13,8901
Polymers13,8901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.731, 40.637, 41.488
Angle α, β, γ (deg.)93.43, 112.66, 101.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein disulfide-isomerase A6 / Endoplasmic reticulum protein 5 / ER protein 5 / ERp5 / Protein disulfide isomerase P5 / ...Endoplasmic reticulum protein 5 / ER protein 5 / ERp5 / Protein disulfide isomerase P5 / Thioredoxin domain-containing protein 7


Mass: 13889.551 Da / Num. of mol.: 2 / Fragment: second catalytic domain, UNP residues 160-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA6, ERP5, P5, TXNDC7 / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q15084, protein disulfide-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1M citric acid, 25% PEG3350, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 17641 / Num. obs: 17069 / % possible obs: 96.76 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rsym value: 0.061 / Net I/σ(I): 15.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1136 / Rsym value: 0.268 / % possible all: 86.01

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EF0

4ef0


Resolution: 1.81→39.41 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.744 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.141 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.219 931 5.2 %RANDOM
Rwork0.17515 ---
obs0.17745 17069 96.76 %-
all-17641 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.858 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.25 Å2-0.73 Å2
2--0.3 Å2-0.21 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.81→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 0 89 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221780
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9432418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8185224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23224.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05915291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6531510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021364
X-RAY DIFFRACTIONr_nbd_refined0.2050.2724
X-RAY DIFFRACTIONr_nbtor_refined0.310.21220
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.26
X-RAY DIFFRACTIONr_mcbond_it1.2261.51138
X-RAY DIFFRACTIONr_mcangle_it2.00521787
X-RAY DIFFRACTIONr_scbond_it2.8763741
X-RAY DIFFRACTIONr_scangle_it4.7564.5629
LS refinement shellResolution: 1.81→1.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 57 -
Rwork0.208 1136 -
obs--86.01 %

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